Schema for all_mrna
  Database: ci1    Primary Table: all_mrna    Row Count: 9,200   Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1192int(10) unsigned range Number of bases that match that aren't repeats
misMatches 6int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 5int(10) unsigned range Number of inserts in target
tBaseInsert 1312int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName AK174651varchar(255) values Query sequence name
qSize 1301int(10) unsigned range Query sequence size
qStart 1int(10) unsigned range Alignment start position in query
qEnd 1199int(10) unsigned range Alignment end position in query
tName Scaffold_1varchar(255) values Target sequence name
tSize 972361int(10) unsigned range Target sequence size
tStart 5494int(10) unsigned range Alignment start position in target
tEnd 8004int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 55,108,118,131,690,96,longblob   Size of each block
qStarts 1,56,164,282,413,1103,longblob   Start of each block in query.
tStarts 5494,5949,6323,6927,7217,7908,longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci1.all_est.qName (via all_mrna.qName)
      ci1.mrnaOrientInfo.name (via all_mrna.qName)
      ci1.refGene.name (via all_mrna.qName)
      ci1.refSeqAli.qName (via all_mrna.qName)
      ci1.xenoMrna.qName (via all_mrna.qName)
      ci1.xenoRefGene.name (via all_mrna.qName)
      ci1.xenoRefSeqAli.qName (via all_mrna.qName)
      hgFixed.gbCdnaInfo.acc (via all_mrna.qName)
      hgFixed.gbMiscDiff.acc (via all_mrna.qName)
      hgFixed.gbSeq.acc (via all_mrna.qName)
      hgFixed.gbWarn.acc (via all_mrna.qName)
      hgFixed.imageClone.acc (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58511926000051312+AK174651130111199Scaffold_197236154948004655,108,118,131,690,96,1,56,164,282,413,1103,5494,5949,6323,6927,7217,7908,
58514884000052839+AK112650151101492Scaffold_197236114723190546174,129,111,148,103,827,0,174,303,414,562,665,14723,15054,15977,16166,17065,18227,
5852247300033142698-AB196473228002280Scaffold_1972361264943146918142,24,16,323,92,149,84,278,197,110,118,117,141,23,92,153,81,137,0,143,167,184,507,599,748,833,1111,1308,1418,1536,1653,1794,1817,1909,2062,2143,26494,26636,26662,26678,27286,27447,27733,27817,28345,28981,29158,29486,29828,30078,30264,30537,31177,31332,
58514681100113734+AK173911149131483Scaffold_197236132355345685155,153,109,836,226,3,158,311,420,1257,32355,32581,33123,33506,34342,
5851824170011972048+AK113411190111861Scaffold_197236160737646268494,151,153,217,92,167,484,83,1,495,646,799,1016,1108,1275,1778,60737,61285,62210,62699,63230,63887,64055,64543,
5851595110000115698+AK116666165801606Scaffold_1972361764838378712126,84,141,131,109,163,143,72,159,126,76,276,0,126,210,351,482,591,754,897,969,1128,1254,1330,76483,76951,77322,77896,78312,78688,79946,80806,81240,82347,83072,83511,
5857016000052277+AK17383574411718Scaffold_19723618080683790672,159,126,76,146,128,11,83,242,368,444,590,80806,81240,82347,83072,83511,83662,
5862260200011139176+AK114499228902281Scaffold_197236113331014476615152,78,123,106,173,120,124,185,127,60,178,136,107,384,227,0,152,230,353,459,632,752,876,1061,1188,1248,1426,1562,1669,2054,133310,133894,134423,135225,135661,137114,137892,138739,139365,140947,142092,142522,143289,144155,144539,
586174519001197284+AK116523177101765Scaffold_197236113571114475911123,120,124,185,127,60,178,136,107,384,220,0,123,243,367,552,679,739,917,1053,1160,1545,135711,137114,137892,138739,139365,140947,142092,142522,143289,144155,144539,
586230510000036819+AB078508233302315Scaffold_19723611495891587234661,127,132,1395,0,661,788,920,149589,154436,154617,157328,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.